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SMTL ID : 6vei.1
Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in Complex with NADPH and AG-881 (Vorasidenib) Inhibitor
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.10 Å
Oligo State
homo-dimer
Ligands
2 x
NDP
:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
(Non-covalent)
NDP.1:
18 residues within 4Å:
Chain A:
T.75
,
I.76
,
T.77
,
R.82
,
N.96
,
L.288
,
G.289
,
A.308
,
H.309
,
G.310
,
T.311
,
V.312
,
T.313
,
R.314
,
H.315
,
T.327
,
N.328
,
D.375
18
PLIP interactions
:
18 interactions with chain A
Hydrogen bonds:
A:T.77
,
A:T.77
,
A:T.77
,
A:R.82
,
A:R.82
,
A:A.308
,
A:G.310
,
A:G.310
,
A:T.311
,
A:V.312
,
A:N.328
,
A:N.328
Water bridges:
A:T.313
,
A:T.313
,
A:A.331
Salt bridges:
A:R.314
,
A:H.315
pi-Stacking:
A:H.309
NDP.8:
23 residues within 4Å:
Chain A:
L.250
,
D.253
,
Q.257
,
K.260
Chain B:
K.72
,
A.74
,
T.75
,
I.76
,
T.77
,
R.82
,
N.96
,
L.288
,
G.289
,
H.309
,
G.310
,
T.311
,
V.312
,
T.313
,
R.314
,
H.315
,
T.327
,
N.328
Ligands:
PEG.10
27
PLIP interactions
:
6 interactions with chain A
,
21 interactions with chain B
Hydrogen bonds:
A:D.253
,
A:Q.257
,
A:Q.257
,
B:K.72
,
B:T.75
,
B:T.77
,
B:T.77
,
B:T.77
,
B:R.82
,
B:R.82
,
B:N.96
,
B:N.96
,
B:G.310
,
B:G.310
,
B:T.311
,
B:V.312
,
B:N.328
,
B:N.328
Water bridges:
A:D.253
,
A:D.253
,
B:T.75
,
B:R.100
,
B:R.314
,
B:A.331
Salt bridges:
A:K.260
,
B:H.315
pi-Stacking:
B:H.309
1 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.2:
7 residues within 4Å:
Chain A:
Y.231
,
D.232
,
K.233
,
Q.234
,
Y.235
,
K.236
,
S.237
6
PLIP interactions
:
6 interactions with chain A
Hydrogen bonds:
A:D.232
,
A:Q.234
,
A:Y.235
,
A:K.236
,
A:S.237
Water bridges:
A:Q.238
1 x
33O
:
3,6,9,12,15,18,21,24,27,30,33,36-dodecaoxaoctatriacontane-1,38-diol
(Non-covalent)
33O.3:
7 residues within 4Å:
Chain A:
R.20
,
I.21
,
E.24
,
L.25
,
E.28
,
E.47
,
Q.320
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:R.20
4 x
PEG
:
DI(HYDROXYETHYL)ETHER
(Non-functional Binders)
PEG.4:
6 residues within 4Å:
Chain A:
M.199
,
S.202
,
V.296
,
G.300
,
H.342
,
K.345
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:S.202
Water bridges:
A:Q.198
,
A:Q.198
,
A:R.338
PEG.5:
6 residues within 4Å:
Chain A:
P.206
,
Y.208
,
S.261
,
G.263
,
G.264
,
F.265
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:Y.208
,
A:G.263
PEG.10:
9 residues within 4Å:
Chain A:
K.212
,
I.215
,
D.252
Chain B:
T.77
,
S.94
,
N.96
,
Y.139
,
D.275
Ligands:
NDP.8
9
PLIP interactions
:
6 interactions with chain B
,
3 interactions with chain A
Hydrogen bonds:
B:T.77
,
B:S.94
,
B:Y.139
,
A:D.252
Water bridges:
B:T.77
,
B:R.100
,
B:R.109
,
A:K.212
,
A:T.214
PEG.11:
6 residues within 4Å:
Chain B:
S.195
,
Q.198
,
M.199
,
S.202
,
V.296
,
P.298
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:S.202
,
B:S.202
,
B:P.298
1 x
ACT
:
ACETATE ION
(Non-functional Binders)
ACT.6:
3 residues within 4Å:
Chain A:
R.222
,
D.225
,
E.229
5
PLIP interactions
:
5 interactions with chain A
Hydrophobic interactions:
A:E.229
Water bridges:
A:R.222
,
A:R.222
,
A:R.222
Salt bridges:
A:R.222
1 x
MLA
:
MALONIC ACID
(Non-covalent)
MLA.7:
5 residues within 4Å:
Chain A:
L.168
,
V.169
,
H.170
Chain B:
R.140
,
Y.183
7
PLIP interactions
:
4 interactions with chain A
,
3 interactions with chain B
Hydrogen bonds:
A:L.168
Water bridges:
A:H.170
,
A:N.171
,
B:T.142
,
B:T.142
Salt bridges:
A:H.170
,
B:R.140
1 x
9UO
:
6-(6-chloropyridin-2-yl)-N2,N4-bis[(2R)-1,1,1-trifluoropropan-2-yl]-1,3,5-triazine-2,4-diamine
(Non-covalent)
9UO.9:
19 residues within 4Å:
Chain A:
W.124
,
V.255
,
M.259
,
Y.272
,
D.273
,
V.276
,
Q.277
,
S.280
,
V.281
Chain B:
W.124
,
V.255
,
A.258
,
M.259
,
W.267
,
D.273
,
V.276
,
Q.277
,
S.280
,
V.281
10
PLIP interactions
:
6 interactions with chain A
,
4 interactions with chain B
Hydrophobic interactions:
A:V.255
,
A:D.273
,
A:V.276
,
A:V.281
Hydrogen bonds:
A:Q.277
,
A:S.280
,
B:Q.277
,
B:Q.277
,
B:S.280
Halogen bonds:
B:D.273
1 x
MLT
:
D-MALATE
(Non-covalent)
MLT.12:
6 residues within 4Å:
Chain A:
R.140
,
T.142
,
Y.183
Chain B:
L.168
,
V.169
,
H.170
5
PLIP interactions
:
4 interactions with chain B
,
1 interactions with chain A
Water bridges:
B:L.168
,
B:H.170
,
B:N.171
Salt bridges:
B:H.170
Hydrogen bonds:
A:Y.183
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Konteatis, Z. et al., Vorasidenib (AG-881): A First-in-Class, Brain-Penetrant Dual Inhibitor of Mutant IDH1 and 2 for Treatment of Glioma. Acs Med.Chem.Lett. (2020)
Release Date
2020-02-05
Peptides
Isocitrate dehydrogenase [NADP] cytoplasmic:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Isocitrate dehydrogenase [NADP] cytoplasmic
Related Entries With Identical Sequence
3inm.1
|
3inm.2
|
4kzo.1
|
4kzo.2
|
4umx.1
|
4umy.1
|
5lge.1
|
5lge.2
|
6adg.1
|
6adg.2
|
6o2z.1
|
6u4j.1
|
6vg0.1
|
6vg0.2
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